Continuity mistake: When Sam is in his bedroom, after he finds the Cube sliver it falls and dramatically burns a hole through the floor into the kitchen. But Sam's bedroom is over the living room (there is nothing on the ground floor below Sam's elevated bathroom, and in the first movie Jazz hides in this open space), and the kitchen is actually located between the den and dining room, at the other end of the house. If they were to follow the actual floor plan of the house, the Cube sliver would have landed in the area of the piano in the living room, but where would the fun have been in that? (00:12:30)
Continuity mistake: While Mikaela and Sam are on the phone with each other (after the failed webchat date the night before), when Wheelie starts reaching up for the safe's combination lock in the first shot, there are no mouse traps on the floor near the short stool to his left, nor are there any cigar boxes. However, in the next shot two mouse traps (a snap trap with cheese bait and a glue trap) and two cigar boxes have all suddenly appeared. Wheelie proceeds to step on the two traps and then stands on the two boxes to reach the combination lock. (00:47:05)
Continuity mistake: After Mikaela throws the metal box at Alice and breaks the window, when Sam runs out of his dorm room screaming we see (and have seen multiple times prior to this) the wall and bathroom door opposite his door. Oddly enough, in the next shot from the hallway, Sam, Mikaela and Leo are actually leaving from a door that's farther down the hallway. Sam's actual door is the first one on the right, opposite the bathroom door - there is a bike wheel leaning against the wall beside the bathroom door. (00:52:00)
Continuity mistake: In Sam's dorm room, there is a white mini fridge at the foot of his bed, flat against the wall under the Cloverfield poster. However, when Sam rushes after Mikaela just as Alice's 'tongue' grabs hold of his neck, that fridge has moved to in front of the closet door, but it moves back to its original position thereafter. (00:50:35 - 00:51:30)
Continuity mistake: The Saturn that Mikaela is driving has a moonroof that encompasses most of the roof, over the front and back seats. When the Decepticon Grindor captures them, in the interior shot looking up at Leo as Grindor seizes the Saturn, the car has a solid roof over Leo, which is also seen in the interior shot as they fall. (00:54:05 - 00:55:05)
Factual error: In the original Transformers, Tyrese Gibson's character is credited as and wears the rank insignia of a USAF Technical Sergeant. In Revenge of the Fallen, set two years later, Gibson's character now wears the insignia of a USAF Chief Master Sergeant, three ranks higher than his rank in the first movie. The USAF would not jump someone three grades into the top 1% of the enlisted force no matter what his heroics or experience (that does not even happen to Medal of Honor awardees). Clearly the screenwriters recognized this as Captain Lennox is bumped only one grade to Major despite his actions in the first film and Gibson's character, as noted in another mistake, is credited as Master Sergeant Epps, a reasonable promotion. The costume department simply got the insignia wrong.
Plot hole: Simmons stands outside the 'The Monastery' at Petra (not to be confused with 'The Al Kazneh' at Petra where Indiana Jones and the Last Crusade was filmed) and looks at the horizon, and he is able to see the Air Force landing with Optimus by the pyramids. It then appears to take them mere minutes to drive over there. This is outright laughable, even accepting that they make the trip in an alien robot car. Petra and Cairo are separated by hundreds of miles of desert, not to mention Israel being between Egypt and Jordan.
Factual error: The team go to the Smithsonian Air and Space Museum's Stephen F. Udvar-Hazy Center, which is located adjacent to Dulles Airport in Virginia - surrounded by rolling green hills - to find a Transformer. When Jetfire breaks out of the museum, beyond the broken door is a large, desert airplane graveyard with large mountains in the background. This appears to be the 309th Aerospace Maintenance and Regeneration Group (309 AMARG), a well known aircraft 'boneyard', located at Davis-Monthan AFB, in Arizona.
Visible crew/equipment: When Ron and Sam are discussing college and girls, in the shot facing Mikaela, as she's airbrushing the design on the motorcycle, the reflection of a crewmember (wearing a blue shirt) holding a reflector screen is visible on the chrome surface at the left, and as the camera pans in closer to her its moving shadow is also visible. (00:10:50)
Continuity mistake: When Sam is on the cell with Mikaela, telling her about the long distance relationship kit, he reaches for the webcam with his right hand outstretched while holding the cell with his left, but in the close-up it's his left hand picking it up, while holding the cell with his right hand. (00:11:20)
Continuity mistake: At the Smithsonian Air and Space Museum, when Mikaela, Sam and Simmons follow Wheelie they reach Jetfire's enclosure with the large information plaque attached to the metal front bar, as Wheelie faces them. Next shot, that whole front horizontal bar is gone along with the information plaque, and Wheelie now faces Jetfire. Then when the Cube shard attaches itself to Jetfire the metal horizontal bar reappears, though the large plaque is still gone, and that bar vanishes once again in the shot from under Jetfire. (01:22:35)
Continuity mistake: Mikaela is wearing high heels when she reaches the stairs, before entering the library. Then in the library, her high heels have vanished and she is suddenly wearing flat shoes in this scene. (00:53:50)